The LucasArts Games Hint Line employee who "helps" you out in the Dinky Island forest is actually based on a real person named Chester who works at LucasArts and specializes in the Hint Line department.
While on Monkey Island, you can use the phone on the tree to call the LucasArts Games Hint Line. One of the questions you can ask the clerk is "who thought up that dumb stump joke?" The clerk responds with "I'm tired of hearing about that damn stump. Do you have any idea how many calls I get a DAY about that? Don't ask me about it again." This refers to an infamous joke in The Secret of Monkey Island (1990), where Guybrush notices a hole in a tree stump, which (he says) leads to a vast maze of caverns below. When the player tries to climb through, the game asks to insert non-existing game discs, and after unsuccessful attempts, Guybrush gives up. The joke was lost on many players, who flooded the Hint Line thinking this was a technical error instead of a deliberate joke.
The only game in the series whose title includes the serial number.
At the beginning of Part 3 when Guybrush steps out of the box, he immediately says "I hate snakes" which is a nod to famous icon Indiana Jones.